The test pairs WGS technology with Clear Labs’ analytics pipeline to enable understanding of how different pathogen and probiotic strains are related, how they are connected evolutionarily, where they come from geographically and with which food groups they are associated.
The WGS test is being used by a global manufacturing company and a national testing lab to monitor pathogen risk across product lines.
Clear Labs said it was targeting 50 major brands by the end of 2017 and having tests resold through three to four multinational testing labs.
It starts at $450 for single sample and decrease with volume, to below $100 for high volume testing.
Proactive instead of reactive
Sasan Amini, CEO and co-founder of Clear Labs, said: “As the food industry shifts to a model that is proactive, instead of reactive, we want the industry to look to Clear Labs for the most reliable, accurate, and cost-effective solutions to help them avoid costly, harmful outbreaks and comply with FSMA.”
Mahni Ghorashi, Clear Labs co-founder, said legacy sequencing has had issues with read length and redundancy.
Clear Labs said the WGS Test can be used:
- To monitor ingredient supplies and effectiveness of preventive and sanitary controls
- To correlate a specific pathogen strain to a specific crop with a specific geographical origin (by comparing the WGS to a comprehensive database of outbreaks strains)
- To develop rapid method- and culture-independent tests
- To determine the persistence of pathogens in the environment
- To monitor emerging pathogens; and as a possible indicator of antimicrobial resistance
“Part of the know-how of Clear Labs' are trade secrets on how to optimize the latest NGS platforms for increasing accuracy and reducing error rate (false positive rates of less than 0.001%),” he told FoodQualityNews.
“This is used for proactive food safety (pathogen) strain applications, and post-recall analysis. Database accuracy remains a problem across the board in any use case (pathogen detection, food fraud, GMOs etc.), as well as NGS – ‘know how’.”
Ghorashi said the next version of the platform, expected by the end of 2017, will feature live/dead distinguishing of pathogens.
The current version has quantification of pathogen strains, the ability to calibrate platform sensitivity for quantification thresholds and can turn on/off different testing applications.
Workflow explained
In terms of workflow, Ghorashi said samples are processed in a lab setting, with DNA extraction and library preparation that place pathogen strains in the context of food ingredients.
“Next, samples are placed on NGS sequencers for whole genome sequencing, where we use proprietary techniques to do a rapid and scalable reading of the genetic footprint of microorganisms, using advanced NGS sequencing techniques," he said.
“Finally, samples are run through Clear Labs' proprietary bioinformatics pipeline for analysis, and are matched against our proprietary curated database for the most accurate and comprehensive strain identification available in the market.
“Our database merges millions of readings from food samples, public databases like FDA's GenomeTrakr, and is curated through machine learning algorithms to improve the accuracy of testing. [It] updates in real-time for our subscription customers, without charge, and is climbing north of two million entries to date.”
The firm said its proprietary workflow features PCR as part of the process so moving from PCR to Clear Labs’ offering involves taking the food samples a few steps further in preparation for NGS sequencing and transferring to the new workflow is ‘relatively seamless’.
Ghorashi said the software platform is end-to-end enabling any player in the industry, be it small manufacturer, retailer or supplier, to interpret results and use NGS sequencing in their supply chain.
“We provide this data analytics platform for companies to have the tech/data to respond to any outbreak or threat," he said.
“With regards to disputes from regulatory agencies, we provide all of this analysis within the company's own firewall, as well as provide encryption methods which allow brands to identify strain matches, but which safeguard them in the event of regulatory subpoena.”
NGS is the "gold-standard" for pathogen strain identification, said Ghorashi.
“Legacy molecular subtyping methods, namely PFGE (pulsed field gel electrophoresis) have limited discriminatory ability for specific serovars. WGS provides significantly improved subtyping and can discriminate isolates that share common PFGE types. PFGE also yields different patterns for isolates that are closely related," he said.
“The challenge industry has faced to date with WGS is with bioinformatics expertise and analysis, and reliable databases for identification, both of which Clear Labs has solved.”
‘Usher in the new era’
Clear Labs has also released a NGS-based microbiome test so customers can associate microbiome data with food ingredients.
The test can be applied to raw ingredients and finished products and human samples and can be used to correlate findings and patterns through Clear Labs’ software analytics platform.
Ghorashi said it is helping usher in the new era of personalized food and diets that rest on optimizing human gut health.
“Our microbiome test allows forward-thinking organizations to begin to understand the relationship between the human microbiome and the microbiome of our food, so that they can determine individual-specific diet plans for optimal health.”
It is in use by a national lab network and research center. The price starts at $250/sample and decreases to tens of dollars per sample at scale.